Multiple sequence alignment - TraesCS4B01G049800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G049800 chr4B 100.000 5662 0 0 1 5662 38285453 38279792 0.000000e+00 10456.0
1 TraesCS4B01G049800 chr4B 86.818 220 8 4 24 243 38276380 38276578 5.710000e-55 226.0
2 TraesCS4B01G049800 chr4B 100.000 29 0 0 1 29 38276335 38276363 3.000000e-03 54.7
3 TraesCS4B01G049800 chr4D 92.650 4354 213 45 889 5194 25991050 25986756 0.000000e+00 6168.0
4 TraesCS4B01G049800 chr4D 88.449 909 36 23 1 895 25991927 25991074 0.000000e+00 1033.0
5 TraesCS4B01G049800 chr4D 87.021 339 21 12 5326 5646 25986333 25986000 1.500000e-95 361.0
6 TraesCS4B01G049800 chr4D 81.746 126 13 6 5202 5326 25986482 25986366 4.670000e-16 97.1
7 TraesCS4B01G049800 chr4D 97.143 35 1 0 24 58 25983441 25983475 6.130000e-05 60.2
8 TraesCS4B01G049800 chr4D 100.000 29 0 0 1 29 25983396 25983424 3.000000e-03 54.7
9 TraesCS4B01G049800 chr4A 97.444 1682 31 6 2217 3889 577230329 577228651 0.000000e+00 2857.0
10 TraesCS4B01G049800 chr4A 91.757 1201 52 19 3826 5004 577228643 577227468 0.000000e+00 1626.0
11 TraesCS4B01G049800 chr4A 80.990 626 36 28 5066 5646 577226985 577226398 2.440000e-113 420.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G049800 chr4B 38279792 38285453 5661 True 10456.000000 10456 100.000000 1 5662 1 chr4B.!!$R1 5661
1 TraesCS4B01G049800 chr4D 25986000 25991927 5927 True 1914.775000 6168 87.466500 1 5646 4 chr4D.!!$R1 5645
2 TraesCS4B01G049800 chr4A 577226398 577230329 3931 True 1634.333333 2857 90.063667 2217 5646 3 chr4A.!!$R1 3429

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
762 777 0.031178 ACTTTCCAGCGACGTTACGT 59.969 50.0 11.12 11.12 45.10 3.57 F
1418 1474 0.319211 CACGACAACCGCTTCACCTA 60.319 55.0 0.00 0.00 43.32 3.08 F
1737 1793 0.373716 GCGGGTCGATTAGCTTTGTG 59.626 55.0 0.00 0.00 0.00 3.33 F
3042 3098 0.548031 ATGAGTACATGCCACAGGGG 59.452 55.0 0.00 0.00 40.85 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1770 0.103208 AAGCTAATCGACCCGCTGAG 59.897 55.000 5.12 0.0 32.22 3.35 R
2481 2537 0.888736 CTGACCCAACAATGACGCCA 60.889 55.000 0.00 0.0 0.00 5.69 R
3090 3146 1.561542 AGTCGCCTCTTCCATTCCAAT 59.438 47.619 0.00 0.0 0.00 3.16 R
5006 5167 0.178301 TAACAACGACCACACAGCCA 59.822 50.000 0.00 0.0 0.00 4.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 73 2.728015 TGCCGCGCATACGATACG 60.728 61.111 8.75 0.00 43.93 3.06
64 74 2.427905 GCCGCGCATACGATACGA 60.428 61.111 8.75 0.00 43.93 3.43
65 75 1.800315 GCCGCGCATACGATACGAT 60.800 57.895 8.75 0.00 43.93 3.73
66 76 0.521867 GCCGCGCATACGATACGATA 60.522 55.000 8.75 0.00 43.93 2.92
67 77 1.177668 CCGCGCATACGATACGATAC 58.822 55.000 8.75 0.00 43.93 2.24
97 107 1.922189 CGTAATTACGGCCAGACGC 59.078 57.895 26.65 0.00 45.30 5.19
122 132 4.410400 CCAGGCCCGGTCCAGAAC 62.410 72.222 3.37 0.00 0.00 3.01
123 133 3.322466 CAGGCCCGGTCCAGAACT 61.322 66.667 3.37 0.00 0.00 3.01
124 134 3.003763 AGGCCCGGTCCAGAACTC 61.004 66.667 3.37 0.00 0.00 3.01
125 135 4.097361 GGCCCGGTCCAGAACTCC 62.097 72.222 0.00 0.00 0.00 3.85
126 136 3.319198 GCCCGGTCCAGAACTCCA 61.319 66.667 0.00 0.00 0.00 3.86
127 137 2.982130 CCCGGTCCAGAACTCCAG 59.018 66.667 0.00 0.00 0.00 3.86
128 138 1.609501 CCCGGTCCAGAACTCCAGA 60.610 63.158 0.00 0.00 0.00 3.86
129 139 0.978146 CCCGGTCCAGAACTCCAGAT 60.978 60.000 0.00 0.00 0.00 2.90
179 189 2.734723 CTGTGCCGTCACCGTCAG 60.735 66.667 0.00 0.00 42.46 3.51
196 206 2.297033 GTCAGAAAAGGCAATTCCAGCA 59.703 45.455 0.00 0.00 37.29 4.41
248 258 5.511088 ACTGAAACGAGCGTTACAAATAG 57.489 39.130 8.82 4.54 37.35 1.73
285 299 1.302511 GAGCACTCCCGAAAAGCCA 60.303 57.895 0.00 0.00 0.00 4.75
314 329 4.410743 GCAGCAGCGCCTTTGGTC 62.411 66.667 2.29 0.00 0.00 4.02
315 330 4.093952 CAGCAGCGCCTTTGGTCG 62.094 66.667 2.29 0.00 0.00 4.79
318 333 4.093952 CAGCGCCTTTGGTCGCAG 62.094 66.667 20.51 12.83 45.36 5.18
322 337 3.793144 GCCTTTGGTCGCAGCGAG 61.793 66.667 20.23 6.41 36.23 5.03
363 378 2.926200 CGTCACAGATCAAGTCCATCAC 59.074 50.000 0.00 0.00 0.00 3.06
456 471 0.802994 CAAACCGCGCATGCATTGAT 60.803 50.000 19.57 0.00 42.97 2.57
457 472 0.108709 AAACCGCGCATGCATTGATT 60.109 45.000 19.57 3.83 42.97 2.57
458 473 0.802994 AACCGCGCATGCATTGATTG 60.803 50.000 19.57 0.00 42.97 2.67
519 534 0.741574 TAACATTACAGGCCACCGCG 60.742 55.000 5.01 0.00 35.02 6.46
568 583 1.107945 GCCTCCACTCTACTCCACTC 58.892 60.000 0.00 0.00 0.00 3.51
571 586 2.374184 CTCCACTCTACTCCACTCCTG 58.626 57.143 0.00 0.00 0.00 3.86
578 593 0.394488 TACTCCACTCCTGCGAGAGG 60.394 60.000 7.62 3.65 45.53 3.69
579 594 3.071206 TCCACTCCTGCGAGAGGC 61.071 66.667 7.62 0.00 44.24 4.70
621 636 3.775654 CCGCCTCCCCAGACAGAC 61.776 72.222 0.00 0.00 0.00 3.51
622 637 2.997315 CGCCTCCCCAGACAGACA 60.997 66.667 0.00 0.00 0.00 3.41
714 729 2.203437 GGTGCGGGTTTCAAGGGT 60.203 61.111 0.00 0.00 0.00 4.34
719 734 1.110518 GCGGGTTTCAAGGGTTTCCA 61.111 55.000 0.00 0.00 34.83 3.53
733 748 1.567208 TTTCCAATCCTAGCCCCGCA 61.567 55.000 0.00 0.00 0.00 5.69
758 773 1.597027 CCCACTTTCCAGCGACGTT 60.597 57.895 0.00 0.00 0.00 3.99
762 777 0.031178 ACTTTCCAGCGACGTTACGT 59.969 50.000 11.12 11.12 45.10 3.57
774 789 1.194495 CGTTACGTATCCAAGACGGC 58.806 55.000 7.22 0.00 44.58 5.68
775 790 1.564207 GTTACGTATCCAAGACGGCC 58.436 55.000 0.00 0.00 44.58 6.13
776 791 0.461135 TTACGTATCCAAGACGGCCC 59.539 55.000 0.00 0.00 44.58 5.80
938 985 1.338655 GCATCCCGAGACTTACTCCTC 59.661 57.143 0.00 0.00 42.18 3.71
955 1002 3.309296 TCCTCTCTCTCTCTCTCTCTCC 58.691 54.545 0.00 0.00 0.00 3.71
956 1003 3.051803 TCCTCTCTCTCTCTCTCTCTCCT 60.052 52.174 0.00 0.00 0.00 3.69
957 1004 3.323403 CCTCTCTCTCTCTCTCTCTCCTC 59.677 56.522 0.00 0.00 0.00 3.71
958 1005 4.222336 CTCTCTCTCTCTCTCTCTCCTCT 58.778 52.174 0.00 0.00 0.00 3.69
959 1006 4.219115 TCTCTCTCTCTCTCTCTCCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
983 1030 2.812619 CCCCCTTCCGCATCTCTCC 61.813 68.421 0.00 0.00 0.00 3.71
991 1038 1.456518 CGCATCTCTCCCCTCTCCA 60.457 63.158 0.00 0.00 0.00 3.86
1017 1064 3.567579 AATGCAGTCCCCCACCGTG 62.568 63.158 0.00 0.00 0.00 4.94
1062 1118 2.456443 GGGATTCCTCCTGGCCCTC 61.456 68.421 0.00 0.00 41.74 4.30
1181 1237 4.821589 GGACAAGGCGCTCTCCGG 62.822 72.222 7.64 0.00 37.44 5.14
1182 1238 3.760035 GACAAGGCGCTCTCCGGA 61.760 66.667 7.64 2.93 37.44 5.14
1183 1239 3.077556 ACAAGGCGCTCTCCGGAT 61.078 61.111 3.57 0.00 37.44 4.18
1184 1240 2.587194 CAAGGCGCTCTCCGGATG 60.587 66.667 3.57 1.79 37.44 3.51
1185 1241 3.854669 AAGGCGCTCTCCGGATGG 61.855 66.667 3.57 1.39 37.44 3.51
1190 1246 4.554036 GCTCTCCGGATGGGGCAC 62.554 72.222 10.58 0.00 34.77 5.01
1261 1317 3.691342 CCGCCGTCCAGGTCAAGA 61.691 66.667 0.00 0.00 43.70 3.02
1334 1390 2.581953 GCGCCTCGAGCTCTTCAG 60.582 66.667 12.85 4.75 40.39 3.02
1387 1443 3.134792 GCCTCGACTCGCTCCAGA 61.135 66.667 0.00 0.00 0.00 3.86
1388 1444 2.485795 GCCTCGACTCGCTCCAGAT 61.486 63.158 0.00 0.00 0.00 2.90
1396 1452 0.820226 CTCGCTCCAGATCCTCAACA 59.180 55.000 0.00 0.00 0.00 3.33
1408 1464 1.156736 CCTCAACATCCACGACAACC 58.843 55.000 0.00 0.00 0.00 3.77
1418 1474 0.319211 CACGACAACCGCTTCACCTA 60.319 55.000 0.00 0.00 43.32 3.08
1427 1483 1.146263 GCTTCACCTACATCCCGGG 59.854 63.158 16.85 16.85 0.00 5.73
1446 1502 1.686428 GGGGATTTCTTCAAGGGGCTC 60.686 57.143 0.00 0.00 0.00 4.70
1486 1542 0.949105 CCTCGACCACAACCCTTTCG 60.949 60.000 0.00 0.00 0.00 3.46
1487 1543 1.566018 CTCGACCACAACCCTTTCGC 61.566 60.000 0.00 0.00 0.00 4.70
1489 1545 2.593436 ACCACAACCCTTTCGCGG 60.593 61.111 6.13 0.00 0.00 6.46
1527 1583 2.179517 CTCGCCGACTGTGTCTCC 59.820 66.667 0.00 0.00 0.00 3.71
1528 1584 3.343788 CTCGCCGACTGTGTCTCCC 62.344 68.421 0.00 0.00 0.00 4.30
1551 1607 0.535102 CCAACTTCTCCGCCAACAGT 60.535 55.000 0.00 0.00 0.00 3.55
1582 1638 4.144703 GGACGCTCCCGGACTTCC 62.145 72.222 0.73 0.32 39.22 3.46
1606 1662 4.899239 CGATGCCGTCCCTCCAGC 62.899 72.222 0.00 0.00 0.00 4.85
1621 1677 0.963856 CCAGCAGCTCAATCTGGCAA 60.964 55.000 0.00 0.00 40.63 4.52
1622 1678 1.103803 CAGCAGCTCAATCTGGCAAT 58.896 50.000 0.00 0.00 34.74 3.56
1629 1685 2.223203 GCTCAATCTGGCAATGAACTCG 60.223 50.000 0.00 0.00 0.00 4.18
1638 1694 0.389817 CAATGAACTCGCTGTCCGGA 60.390 55.000 0.00 0.00 37.59 5.14
1641 1697 3.644399 GAACTCGCTGTCCGGACCC 62.644 68.421 31.19 20.43 37.59 4.46
1693 1749 1.739562 GAGGTGCTCTGGCTCAACG 60.740 63.158 0.00 0.00 39.59 4.10
1694 1750 2.743928 GGTGCTCTGGCTCAACGG 60.744 66.667 0.00 0.00 39.59 4.44
1695 1751 3.426568 GTGCTCTGGCTCAACGGC 61.427 66.667 0.00 0.00 39.59 5.68
1714 1770 3.782443 AGAATGGGACCGACCGCC 61.782 66.667 0.00 0.00 40.11 6.13
1734 1790 0.535335 TCAGCGGGTCGATTAGCTTT 59.465 50.000 8.43 0.00 37.94 3.51
1737 1793 0.373716 GCGGGTCGATTAGCTTTGTG 59.626 55.000 0.00 0.00 0.00 3.33
1743 1799 1.810151 TCGATTAGCTTTGTGGCCAAC 59.190 47.619 7.24 2.03 0.00 3.77
1744 1800 1.135402 CGATTAGCTTTGTGGCCAACC 60.135 52.381 7.24 0.00 0.00 3.77
1749 1805 1.109323 GCTTTGTGGCCAACCTGACT 61.109 55.000 7.24 0.00 36.63 3.41
1781 1837 4.030452 GTGGCTGCACTCCAACGC 62.030 66.667 0.50 0.00 35.01 4.84
1811 1867 2.125512 CTTGCCGGACTTCTCGGG 60.126 66.667 5.05 0.00 46.86 5.14
1835 1891 2.452600 ACCAGCCTTTTTGAGTTGGA 57.547 45.000 0.00 0.00 34.19 3.53
1842 1898 2.749621 CCTTTTTGAGTTGGATCTCCGG 59.250 50.000 0.00 0.00 39.43 5.14
1862 1918 2.358737 CAACCAGCTCACCGGTCC 60.359 66.667 2.59 0.00 33.17 4.46
1863 1919 4.003788 AACCAGCTCACCGGTCCG 62.004 66.667 2.59 3.60 33.17 4.79
1887 1943 1.517242 CAGCCAGTCTTGTCAACCTC 58.483 55.000 0.00 0.00 0.00 3.85
1901 1957 4.405680 TGTCAACCTCAAGTCTCTGAAGAA 59.594 41.667 0.00 0.00 31.93 2.52
1902 1958 5.070981 TGTCAACCTCAAGTCTCTGAAGAAT 59.929 40.000 0.00 0.00 31.93 2.40
1937 1993 1.244019 AATTTGCTGCAGGGACCGAC 61.244 55.000 17.12 0.00 0.00 4.79
1959 2015 1.242076 CCAACTTTGCTCCCTCTGTG 58.758 55.000 0.00 0.00 0.00 3.66
1970 2026 2.104792 CTCCCTCTGTGGAAGTTGACAA 59.895 50.000 0.00 0.00 38.35 3.18
1972 2028 2.158755 CCCTCTGTGGAAGTTGACAAGT 60.159 50.000 0.00 0.00 38.35 3.16
1973 2029 3.134458 CCTCTGTGGAAGTTGACAAGTC 58.866 50.000 0.00 0.00 38.35 3.01
1974 2030 2.797156 CTCTGTGGAAGTTGACAAGTCG 59.203 50.000 0.00 0.00 0.00 4.18
1975 2031 1.867233 CTGTGGAAGTTGACAAGTCGG 59.133 52.381 0.00 0.00 0.00 4.79
2117 2173 1.001746 CGACCCATGCAGATATCAGCT 59.998 52.381 19.41 4.34 0.00 4.24
2151 2207 6.353404 TGTGATAGTGGTAAGAACATCACA 57.647 37.500 10.30 10.30 45.93 3.58
2205 2261 1.898472 AGCATCTCACCATCTATCGGG 59.102 52.381 0.00 0.00 0.00 5.14
2481 2537 3.558109 GCAACAAGGCTTCCTCTTCTACT 60.558 47.826 0.00 0.00 30.89 2.57
3042 3098 0.548031 ATGAGTACATGCCACAGGGG 59.452 55.000 0.00 0.00 40.85 4.79
3090 3146 3.456280 GAAAGAACACAATTTGCAGCCA 58.544 40.909 0.00 0.00 0.00 4.75
3359 3415 3.058224 GGTGAGCATCCCGTATATTTTGC 60.058 47.826 0.00 0.00 0.00 3.68
3380 3436 3.425492 GCGCTTCACTTTTCTGATTCTCC 60.425 47.826 0.00 0.00 0.00 3.71
3673 3731 7.415592 TCAATTCAGTGATCTACTCTGATGT 57.584 36.000 0.00 0.00 44.77 3.06
3852 3919 7.119407 ACAAACATGTTCATGAGAAGATCTCTG 59.881 37.037 12.39 3.01 43.73 3.35
3867 4005 1.352882 CTCTGTCGCAAGCTGAGCTG 61.353 60.000 8.16 3.43 39.62 4.24
3910 4048 1.972588 ACTTCCAATAGCCCCAGACT 58.027 50.000 0.00 0.00 0.00 3.24
3948 4087 1.616159 TTTTACCTTCAGCTGGTGCC 58.384 50.000 15.13 0.00 40.80 5.01
3956 4095 2.519302 AGCTGGTGCCGCAACTTT 60.519 55.556 10.37 0.00 40.80 2.66
3964 4103 0.179059 TGCCGCAACTTTCTGTCAGA 60.179 50.000 0.00 0.00 0.00 3.27
3966 4105 1.537202 GCCGCAACTTTCTGTCAGAAT 59.463 47.619 15.95 0.00 33.67 2.40
3970 4109 4.328440 CCGCAACTTTCTGTCAGAATCTAG 59.672 45.833 15.95 12.64 33.67 2.43
4109 4248 8.559536 CCACTTGCAATACCTGTATAATAACTG 58.440 37.037 0.00 0.00 0.00 3.16
4139 4279 4.207165 ACATCTTTTGTGCAGTTACTGGT 58.793 39.130 14.63 0.00 37.11 4.00
4298 4438 3.270027 CAATGATACGTTCCAGAAGGCA 58.730 45.455 0.00 0.00 33.74 4.75
4310 4450 2.146342 CAGAAGGCAATCGACACAACT 58.854 47.619 0.00 0.00 0.00 3.16
4436 4576 1.374758 CAACGTGCTCTCCACCCTC 60.375 63.158 0.00 0.00 41.53 4.30
4451 4591 0.247736 CCCTCTCGGAAGTGTGGAAG 59.752 60.000 0.00 0.00 39.79 3.46
4535 4675 1.475682 CTGAAGAAATGGCAGGCCTTC 59.524 52.381 0.00 0.00 36.94 3.46
4556 4696 0.254178 AGGACAGCAGCCATTTCGAT 59.746 50.000 0.00 0.00 0.00 3.59
4698 4844 1.810441 CCAGAAGCTCTGCTCGCTG 60.810 63.158 12.39 12.39 42.98 5.18
4737 4884 6.319048 TCATTCATTCCTTTAGCCTCTTCT 57.681 37.500 0.00 0.00 0.00 2.85
4738 4885 6.725364 TCATTCATTCCTTTAGCCTCTTCTT 58.275 36.000 0.00 0.00 0.00 2.52
4740 4887 5.762179 TCATTCCTTTAGCCTCTTCTTCA 57.238 39.130 0.00 0.00 0.00 3.02
4741 4888 6.126863 TCATTCCTTTAGCCTCTTCTTCAA 57.873 37.500 0.00 0.00 0.00 2.69
4742 4889 5.940470 TCATTCCTTTAGCCTCTTCTTCAAC 59.060 40.000 0.00 0.00 0.00 3.18
4745 4892 3.348119 CTTTAGCCTCTTCTTCAACCCC 58.652 50.000 0.00 0.00 0.00 4.95
4746 4893 1.286248 TAGCCTCTTCTTCAACCCCC 58.714 55.000 0.00 0.00 0.00 5.40
4767 4914 3.093172 CCCTCCCTCCCTGCCTTC 61.093 72.222 0.00 0.00 0.00 3.46
4777 4924 2.424956 CTCCCTGCCTTCTAAATGTTGC 59.575 50.000 0.00 0.00 0.00 4.17
4789 4936 0.614812 AATGTTGCTGGATTTGGCCC 59.385 50.000 0.00 0.00 0.00 5.80
4819 4966 1.825090 TGCCATGTTAGCTGTCCTTG 58.175 50.000 0.00 0.00 0.00 3.61
4923 5084 7.456902 TGAACCTAAGTAGAAGATTGTTAGGGT 59.543 37.037 10.42 4.31 42.36 4.34
4934 5095 3.810310 TTGTTAGGGTTTGTTGGCTTG 57.190 42.857 0.00 0.00 0.00 4.01
4935 5096 2.741145 TGTTAGGGTTTGTTGGCTTGT 58.259 42.857 0.00 0.00 0.00 3.16
4936 5097 3.899726 TGTTAGGGTTTGTTGGCTTGTA 58.100 40.909 0.00 0.00 0.00 2.41
4937 5098 3.633065 TGTTAGGGTTTGTTGGCTTGTAC 59.367 43.478 0.00 0.00 0.00 2.90
5027 5188 1.877443 GGCTGTGTGGTCGTTGTTATT 59.123 47.619 0.00 0.00 0.00 1.40
5034 5195 3.754323 TGTGGTCGTTGTTATTCAATCCC 59.246 43.478 0.00 0.00 38.38 3.85
5039 5200 6.090783 GGTCGTTGTTATTCAATCCCTTTTC 58.909 40.000 0.00 0.00 38.38 2.29
5040 5201 6.072119 GGTCGTTGTTATTCAATCCCTTTTCT 60.072 38.462 0.00 0.00 38.38 2.52
5041 5202 7.021790 GTCGTTGTTATTCAATCCCTTTTCTC 58.978 38.462 0.00 0.00 38.38 2.87
5054 5215 2.290577 CCTTTTCTCCTTCCTGGGACTG 60.291 54.545 0.00 0.00 36.20 3.51
5070 5242 1.208052 GACTGTCATGAGCCAGCCTTA 59.792 52.381 12.08 0.00 31.76 2.69
5071 5243 1.065854 ACTGTCATGAGCCAGCCTTAC 60.066 52.381 12.08 0.00 31.76 2.34
5072 5244 0.253044 TGTCATGAGCCAGCCTTACC 59.747 55.000 0.00 0.00 0.00 2.85
5073 5245 0.543749 GTCATGAGCCAGCCTTACCT 59.456 55.000 0.00 0.00 0.00 3.08
5074 5246 0.833287 TCATGAGCCAGCCTTACCTC 59.167 55.000 0.00 0.00 0.00 3.85
5075 5247 0.179034 CATGAGCCAGCCTTACCTCC 60.179 60.000 0.00 0.00 0.00 4.30
5078 5686 0.107643 GAGCCAGCCTTACCTCCATC 59.892 60.000 0.00 0.00 0.00 3.51
5144 5755 1.002684 GATAGACGCTACACCCTGTCG 60.003 57.143 0.00 0.00 36.49 4.35
5145 5756 0.321919 TAGACGCTACACCCTGTCGT 60.322 55.000 0.00 0.00 34.25 4.34
5146 5757 1.443872 GACGCTACACCCTGTCGTG 60.444 63.158 0.00 0.00 32.20 4.35
5148 5759 1.443872 CGCTACACCCTGTCGTGTC 60.444 63.158 0.00 0.00 43.50 3.67
5149 5760 1.863662 CGCTACACCCTGTCGTGTCT 61.864 60.000 0.00 0.00 43.50 3.41
5150 5761 1.171308 GCTACACCCTGTCGTGTCTA 58.829 55.000 0.00 0.00 43.50 2.59
5151 5762 1.132643 GCTACACCCTGTCGTGTCTAG 59.867 57.143 0.00 0.00 43.50 2.43
5152 5763 1.132643 CTACACCCTGTCGTGTCTAGC 59.867 57.143 0.00 0.00 43.50 3.42
5236 6113 2.082231 CAGTGAGCATCCCAGTCTTTG 58.918 52.381 0.00 0.00 0.00 2.77
5265 6142 0.875059 GCCAGCTAATCCGGCATTAC 59.125 55.000 7.12 0.00 45.52 1.89
5266 6143 1.813862 GCCAGCTAATCCGGCATTACA 60.814 52.381 7.12 0.00 45.52 2.41
5267 6144 2.571212 CCAGCTAATCCGGCATTACAA 58.429 47.619 0.00 0.00 0.00 2.41
5269 6146 3.380004 CCAGCTAATCCGGCATTACAAAA 59.620 43.478 0.00 0.00 0.00 2.44
5296 6222 9.802039 AAATTACTTATAAAGTTGGTGGTCTGA 57.198 29.630 0.00 0.00 42.81 3.27
5297 6223 9.975218 AATTACTTATAAAGTTGGTGGTCTGAT 57.025 29.630 0.00 0.00 42.81 2.90
5298 6224 9.614792 ATTACTTATAAAGTTGGTGGTCTGATC 57.385 33.333 0.00 0.00 42.81 2.92
5299 6225 7.259088 ACTTATAAAGTTGGTGGTCTGATCT 57.741 36.000 0.00 0.00 39.04 2.75
5300 6226 7.331791 ACTTATAAAGTTGGTGGTCTGATCTC 58.668 38.462 0.00 0.00 39.04 2.75
5302 6228 3.692257 AAGTTGGTGGTCTGATCTCTG 57.308 47.619 0.00 0.00 0.00 3.35
5303 6229 2.894731 AGTTGGTGGTCTGATCTCTGA 58.105 47.619 0.00 0.00 0.00 3.27
5304 6230 3.448934 AGTTGGTGGTCTGATCTCTGAT 58.551 45.455 0.00 0.00 0.00 2.90
5305 6231 3.197333 AGTTGGTGGTCTGATCTCTGATG 59.803 47.826 0.00 0.00 0.00 3.07
5306 6232 2.113807 TGGTGGTCTGATCTCTGATGG 58.886 52.381 0.00 0.00 0.00 3.51
5307 6233 1.202627 GGTGGTCTGATCTCTGATGGC 60.203 57.143 0.00 0.00 0.00 4.40
5308 6234 1.126488 TGGTCTGATCTCTGATGGCC 58.874 55.000 0.00 0.00 0.00 5.36
5309 6235 1.343782 TGGTCTGATCTCTGATGGCCT 60.344 52.381 3.32 0.00 0.00 5.19
5310 6236 1.767681 GGTCTGATCTCTGATGGCCTT 59.232 52.381 3.32 0.00 0.00 4.35
5311 6237 2.968574 GGTCTGATCTCTGATGGCCTTA 59.031 50.000 3.32 0.00 0.00 2.69
5312 6238 3.006752 GGTCTGATCTCTGATGGCCTTAG 59.993 52.174 3.32 0.00 0.00 2.18
5313 6239 3.894427 GTCTGATCTCTGATGGCCTTAGA 59.106 47.826 3.32 4.08 0.00 2.10
5314 6240 4.527816 GTCTGATCTCTGATGGCCTTAGAT 59.472 45.833 3.32 2.97 0.00 1.98
5315 6241 5.011943 GTCTGATCTCTGATGGCCTTAGATT 59.988 44.000 3.32 0.00 0.00 2.40
5316 6242 5.605908 TCTGATCTCTGATGGCCTTAGATTT 59.394 40.000 3.32 0.00 0.00 2.17
5317 6243 5.618236 TGATCTCTGATGGCCTTAGATTTG 58.382 41.667 3.32 0.00 0.00 2.32
5318 6244 4.428294 TCTCTGATGGCCTTAGATTTGG 57.572 45.455 3.32 0.00 0.00 3.28
5319 6245 3.137176 TCTCTGATGGCCTTAGATTTGGG 59.863 47.826 3.32 0.00 0.00 4.12
5320 6246 3.122480 TCTGATGGCCTTAGATTTGGGA 58.878 45.455 3.32 0.00 0.00 4.37
5321 6247 3.723681 TCTGATGGCCTTAGATTTGGGAT 59.276 43.478 3.32 0.00 0.00 3.85
5322 6248 4.077822 CTGATGGCCTTAGATTTGGGATC 58.922 47.826 3.32 0.00 0.00 3.36
5323 6249 3.462954 TGATGGCCTTAGATTTGGGATCA 59.537 43.478 3.32 0.00 0.00 2.92
5324 6250 3.582998 TGGCCTTAGATTTGGGATCAG 57.417 47.619 3.32 0.00 0.00 2.90
5409 6335 6.632035 CGCCTACTACAACTAAGATAAGAACG 59.368 42.308 0.00 0.00 0.00 3.95
5415 6341 7.828223 ACTACAACTAAGATAAGAACGAGAGGA 59.172 37.037 0.00 0.00 0.00 3.71
5416 6342 7.090953 ACAACTAAGATAAGAACGAGAGGAG 57.909 40.000 0.00 0.00 0.00 3.69
5418 6344 4.581409 ACTAAGATAAGAACGAGAGGAGGC 59.419 45.833 0.00 0.00 0.00 4.70
5419 6345 2.312390 AGATAAGAACGAGAGGAGGCC 58.688 52.381 0.00 0.00 0.00 5.19
5440 6379 2.222508 CGAATGATCAAACGACGTGACC 60.223 50.000 16.27 0.00 0.00 4.02
5443 6382 1.349259 GATCAAACGACGTGACCCGG 61.349 60.000 0.00 0.00 42.24 5.73
5453 6392 1.366366 GTGACCCGGGTCCGATATG 59.634 63.158 43.35 9.16 43.97 1.78
5466 6405 4.142600 GGTCCGATATGAAATGCTTATGCC 60.143 45.833 0.00 0.00 38.71 4.40
5469 6408 5.874810 TCCGATATGAAATGCTTATGCCTAC 59.125 40.000 0.00 0.00 38.71 3.18
5482 6421 6.100004 GCTTATGCCTACTCTAATAATGCGA 58.900 40.000 0.00 0.00 0.00 5.10
5486 6425 4.106197 GCCTACTCTAATAATGCGATCCG 58.894 47.826 0.00 0.00 0.00 4.18
5491 6431 5.467705 ACTCTAATAATGCGATCCGGTTAC 58.532 41.667 0.00 0.00 0.00 2.50
5507 6447 3.693382 TACAGTGATGGCGACGCGG 62.693 63.158 14.61 0.00 0.00 6.46
5557 6500 0.866427 TCGCACGCCAAATTAAACGA 59.134 45.000 0.00 0.00 0.00 3.85
5588 6535 2.616842 GCGTATATTTTCTGGTGGTGGG 59.383 50.000 0.00 0.00 0.00 4.61
5595 6542 3.174987 CTGGTGGTGGGTGGTGGA 61.175 66.667 0.00 0.00 0.00 4.02
5596 6543 2.451493 TGGTGGTGGGTGGTGGAT 60.451 61.111 0.00 0.00 0.00 3.41
5597 6544 2.035626 GGTGGTGGGTGGTGGATG 59.964 66.667 0.00 0.00 0.00 3.51
5598 6545 2.035626 GTGGTGGGTGGTGGATGG 59.964 66.667 0.00 0.00 0.00 3.51
5599 6546 2.451493 TGGTGGGTGGTGGATGGT 60.451 61.111 0.00 0.00 0.00 3.55
5600 6547 2.035626 GGTGGGTGGTGGATGGTG 59.964 66.667 0.00 0.00 0.00 4.17
5646 6593 1.734477 CTTCTCGCTGTCCACACCG 60.734 63.158 0.00 0.00 0.00 4.94
5647 6594 3.220999 TTCTCGCTGTCCACACCGG 62.221 63.158 0.00 0.00 0.00 5.28
5648 6595 3.991051 CTCGCTGTCCACACCGGT 61.991 66.667 0.00 0.00 35.57 5.28
5649 6596 3.916392 CTCGCTGTCCACACCGGTC 62.916 68.421 2.59 0.00 35.57 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 131 3.023949 GCTGGCGACCATCTGGAGT 62.024 63.158 2.55 0.00 38.94 3.85
122 132 2.202987 GCTGGCGACCATCTGGAG 60.203 66.667 2.55 0.00 38.94 3.86
123 133 3.785859 GGCTGGCGACCATCTGGA 61.786 66.667 2.55 0.00 38.94 3.86
124 134 4.100084 TGGCTGGCGACCATCTGG 62.100 66.667 0.00 0.00 42.17 3.86
125 135 2.513204 CTGGCTGGCGACCATCTG 60.513 66.667 0.00 0.00 36.36 2.90
126 136 4.479993 GCTGGCTGGCGACCATCT 62.480 66.667 0.00 0.00 36.36 2.90
179 189 2.071540 GCTTGCTGGAATTGCCTTTTC 58.928 47.619 0.00 0.00 37.63 2.29
233 243 4.708601 ACAAAAGCTATTTGTAACGCTCG 58.291 39.130 19.03 0.00 40.47 5.03
248 258 1.613437 TCCTTGCTAGCCAACAAAAGC 59.387 47.619 13.29 0.00 35.51 3.51
337 352 1.296392 CTTGATCTGTGACGGCCCA 59.704 57.895 0.00 0.00 0.00 5.36
338 353 0.741221 GACTTGATCTGTGACGGCCC 60.741 60.000 0.00 0.00 0.00 5.80
426 441 4.114997 CGGTTTGTGGCGGGATGC 62.115 66.667 0.00 0.00 45.38 3.91
436 451 1.733758 CAATGCATGCGCGGTTTGT 60.734 52.632 14.09 0.00 42.97 2.83
493 508 2.230992 TGGCCTGTAATGTTACGTACGT 59.769 45.455 25.98 25.98 36.45 3.57
502 517 2.435938 CGCGGTGGCCTGTAATGT 60.436 61.111 3.32 0.00 35.02 2.71
503 518 3.202001 CCGCGGTGGCCTGTAATG 61.202 66.667 19.50 0.00 35.02 1.90
504 519 3.395702 TCCGCGGTGGCCTGTAAT 61.396 61.111 27.15 0.00 37.80 1.89
505 520 4.382320 GTCCGCGGTGGCCTGTAA 62.382 66.667 27.15 0.00 37.80 2.41
571 586 4.863925 GAGACGCCTGCCTCTCGC 62.864 72.222 3.05 0.00 38.31 5.03
578 593 2.027751 GGTATCCGAGACGCCTGC 59.972 66.667 0.00 0.00 0.00 4.85
579 594 1.797211 GAGGGTATCCGAGACGCCTG 61.797 65.000 6.60 0.00 38.33 4.85
580 595 1.528776 GAGGGTATCCGAGACGCCT 60.529 63.158 6.60 5.00 38.33 5.52
581 596 1.517210 GAGAGGGTATCCGAGACGCC 61.517 65.000 6.60 0.39 38.33 5.68
582 597 1.517210 GGAGAGGGTATCCGAGACGC 61.517 65.000 2.13 2.13 38.33 5.19
621 636 2.044551 GGCTTCTGCTTCCCCCTG 60.045 66.667 0.00 0.00 39.59 4.45
622 637 3.342477 GGGCTTCTGCTTCCCCCT 61.342 66.667 0.00 0.00 39.59 4.79
703 718 3.239449 AGGATTGGAAACCCTTGAAACC 58.761 45.455 0.00 0.00 34.64 3.27
714 729 1.226262 GCGGGGCTAGGATTGGAAA 59.774 57.895 0.00 0.00 0.00 3.13
719 734 3.878667 GGCTGCGGGGCTAGGATT 61.879 66.667 0.00 0.00 37.53 3.01
745 760 2.518949 GATACGTAACGTCGCTGGAAA 58.481 47.619 0.00 0.00 41.54 3.13
746 761 1.202177 GGATACGTAACGTCGCTGGAA 60.202 52.381 0.00 0.00 41.54 3.53
747 762 0.378257 GGATACGTAACGTCGCTGGA 59.622 55.000 0.00 0.00 41.54 3.86
758 773 1.394266 GGGGCCGTCTTGGATACGTA 61.394 60.000 0.00 0.00 42.00 3.57
877 892 0.980231 GAGAGAGAGGGCACATGGGT 60.980 60.000 0.00 0.00 0.00 4.51
879 894 0.752054 GAGAGAGAGAGGGCACATGG 59.248 60.000 0.00 0.00 0.00 3.66
938 985 4.222336 AGAGAGGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
983 1030 2.971598 ATTGCGGTGGTGGAGAGGG 61.972 63.158 0.00 0.00 0.00 4.30
1164 1220 4.821589 CCGGAGAGCGCCTTGTCC 62.822 72.222 2.29 2.72 0.00 4.02
1168 1224 3.854669 CCATCCGGAGAGCGCCTT 61.855 66.667 11.34 0.00 0.00 4.35
1174 1230 3.866582 GGTGCCCCATCCGGAGAG 61.867 72.222 11.34 4.82 0.00 3.20
1247 1303 1.873591 CTTTGTTCTTGACCTGGACGG 59.126 52.381 0.00 0.00 39.35 4.79
1261 1317 2.115266 CCCCGTCAGGCCTTTGTT 59.885 61.111 0.00 0.00 35.76 2.83
1384 1440 2.094026 TGTCGTGGATGTTGAGGATCTG 60.094 50.000 0.00 0.00 34.92 2.90
1387 1443 2.615493 GGTTGTCGTGGATGTTGAGGAT 60.615 50.000 0.00 0.00 0.00 3.24
1388 1444 1.270625 GGTTGTCGTGGATGTTGAGGA 60.271 52.381 0.00 0.00 0.00 3.71
1396 1452 0.949105 GTGAAGCGGTTGTCGTGGAT 60.949 55.000 3.70 0.00 41.72 3.41
1408 1464 1.227263 CCGGGATGTAGGTGAAGCG 60.227 63.158 0.00 0.00 0.00 4.68
1427 1483 1.005924 TGAGCCCCTTGAAGAAATCCC 59.994 52.381 0.00 0.00 0.00 3.85
1446 1502 4.379243 ACCTCCTTGAGCGCGGTG 62.379 66.667 18.92 0.00 0.00 4.94
1514 1570 1.587054 GTGAGGGAGACACAGTCGG 59.413 63.158 0.00 0.00 37.67 4.79
1515 1571 1.179174 TGGTGAGGGAGACACAGTCG 61.179 60.000 0.00 0.00 39.65 4.18
1521 1577 1.971357 GAGAAGTTGGTGAGGGAGACA 59.029 52.381 0.00 0.00 0.00 3.41
1522 1578 1.276705 GGAGAAGTTGGTGAGGGAGAC 59.723 57.143 0.00 0.00 0.00 3.36
1523 1579 1.645710 GGAGAAGTTGGTGAGGGAGA 58.354 55.000 0.00 0.00 0.00 3.71
1524 1580 0.247736 CGGAGAAGTTGGTGAGGGAG 59.752 60.000 0.00 0.00 0.00 4.30
1527 1583 1.376037 GGCGGAGAAGTTGGTGAGG 60.376 63.158 0.00 0.00 0.00 3.86
1528 1584 0.250295 TTGGCGGAGAAGTTGGTGAG 60.250 55.000 0.00 0.00 0.00 3.51
1606 1662 2.753452 AGTTCATTGCCAGATTGAGCTG 59.247 45.455 0.00 0.00 30.96 4.24
1621 1677 1.215647 GTCCGGACAGCGAGTTCAT 59.784 57.895 29.75 0.00 0.00 2.57
1622 1678 2.649034 GTCCGGACAGCGAGTTCA 59.351 61.111 29.75 0.00 0.00 3.18
1662 1718 4.052229 ACCTCAAGGGACGTCGCG 62.052 66.667 24.68 13.22 40.27 5.87
1666 1722 1.534235 AGAGCACCTCAAGGGACGT 60.534 57.895 0.29 0.00 40.27 4.34
1669 1725 2.596851 GCCAGAGCACCTCAAGGGA 61.597 63.158 0.29 0.00 40.27 4.20
1670 1726 2.045536 GCCAGAGCACCTCAAGGG 60.046 66.667 0.29 0.00 40.27 3.95
1671 1727 1.078567 GAGCCAGAGCACCTCAAGG 60.079 63.158 0.00 0.00 43.56 3.61
1693 1749 2.124695 GTCGGTCCCATTCTGGCC 60.125 66.667 0.00 0.00 35.79 5.36
1694 1750 2.124695 GGTCGGTCCCATTCTGGC 60.125 66.667 0.00 0.00 35.79 4.85
1695 1751 2.186903 CGGTCGGTCCCATTCTGG 59.813 66.667 0.00 0.00 37.25 3.86
1696 1752 2.511600 GCGGTCGGTCCCATTCTG 60.512 66.667 0.00 0.00 0.00 3.02
1698 1754 3.735037 GAGGCGGTCGGTCCCATTC 62.735 68.421 0.00 0.00 0.00 2.67
1714 1770 0.103208 AAGCTAATCGACCCGCTGAG 59.897 55.000 5.12 0.00 32.22 3.35
1734 1790 0.400213 CCTTAGTCAGGTTGGCCACA 59.600 55.000 3.88 0.00 37.99 4.17
1749 1805 1.005037 CCACAGCTGCGTGACCTTA 60.005 57.895 15.27 0.00 39.34 2.69
1826 1882 0.902531 GTCCCGGAGATCCAACTCAA 59.097 55.000 0.73 0.00 38.51 3.02
1830 1886 0.392595 GGTTGTCCCGGAGATCCAAC 60.393 60.000 0.73 10.00 35.14 3.77
1835 1891 1.613630 AGCTGGTTGTCCCGGAGAT 60.614 57.895 0.73 0.00 42.95 2.75
1842 1898 2.358737 CCGGTGAGCTGGTTGTCC 60.359 66.667 0.00 0.00 36.39 4.02
1862 1918 3.052082 CAAGACTGGCTGGCACCG 61.052 66.667 0.00 0.00 0.00 4.94
1863 1919 1.968540 GACAAGACTGGCTGGCACC 60.969 63.158 0.00 0.00 0.00 5.01
1871 1927 3.134458 GACTTGAGGTTGACAAGACTGG 58.866 50.000 13.34 0.00 44.92 4.00
1887 1943 3.683822 GGCTCACATTCTTCAGAGACTTG 59.316 47.826 0.00 0.00 33.34 3.16
1901 1957 0.706433 ATTGTTCCCCAGGCTCACAT 59.294 50.000 0.00 0.00 0.00 3.21
1902 1958 0.482446 AATTGTTCCCCAGGCTCACA 59.518 50.000 0.00 0.00 0.00 3.58
1937 1993 0.695347 AGAGGGAGCAAAGTTGGGAG 59.305 55.000 0.00 0.00 0.00 4.30
1959 2015 1.566018 CCGCCGACTTGTCAACTTCC 61.566 60.000 1.59 0.00 0.00 3.46
1970 2026 2.188062 TTGATTTTTACCCGCCGACT 57.812 45.000 0.00 0.00 0.00 4.18
1972 2028 3.127895 CAGAATTGATTTTTACCCGCCGA 59.872 43.478 0.00 0.00 0.00 5.54
1973 2029 3.434637 CAGAATTGATTTTTACCCGCCG 58.565 45.455 0.00 0.00 0.00 6.46
1974 2030 3.119137 AGCAGAATTGATTTTTACCCGCC 60.119 43.478 0.00 0.00 0.00 6.13
1975 2031 4.110036 AGCAGAATTGATTTTTACCCGC 57.890 40.909 0.00 0.00 0.00 6.13
2109 2165 2.104792 ACATACAACGCCCAGCTGATAT 59.895 45.455 17.39 0.00 0.00 1.63
2117 2173 2.419436 CCACTATCACATACAACGCCCA 60.419 50.000 0.00 0.00 0.00 5.36
2151 2207 3.685756 CCATTTTGGCAAAATTCAGCGAT 59.314 39.130 30.19 9.98 38.97 4.58
2205 2261 3.427233 GCATCTGAAGTGTGGCAATCTTC 60.427 47.826 19.34 19.34 38.30 2.87
2481 2537 0.888736 CTGACCCAACAATGACGCCA 60.889 55.000 0.00 0.00 0.00 5.69
3042 3098 2.113986 AGGTGTTGGCTCACTGGC 59.886 61.111 11.60 0.00 38.28 4.85
3090 3146 1.561542 AGTCGCCTCTTCCATTCCAAT 59.438 47.619 0.00 0.00 0.00 3.16
3359 3415 3.999663 AGGAGAATCAGAAAAGTGAAGCG 59.000 43.478 0.00 0.00 36.25 4.68
3673 3731 2.486548 GGACCAACTAAGGACACAAGCA 60.487 50.000 0.00 0.00 0.00 3.91
3852 3919 0.801251 AAATCAGCTCAGCTTGCGAC 59.199 50.000 0.00 0.00 36.40 5.19
3948 4087 5.164233 TCTAGATTCTGACAGAAAGTTGCG 58.836 41.667 21.29 8.62 37.82 4.85
4109 4248 5.831997 ACTGCACAAAAGATGTTAGGTTTC 58.168 37.500 0.00 0.00 41.46 2.78
4127 4267 0.747852 TCACACGACCAGTAACTGCA 59.252 50.000 0.00 0.00 0.00 4.41
4211 4351 1.417517 TCAGGCTGTGTGTCATCAAGT 59.582 47.619 15.27 0.00 0.00 3.16
4298 4438 4.082408 TCAAGGTCGATAGTTGTGTCGATT 60.082 41.667 0.63 0.00 46.39 3.34
4310 4450 3.117474 AGGTCTCCTCATCAAGGTCGATA 60.117 47.826 0.00 0.00 46.32 2.92
4436 4576 1.376037 GGGCTTCCACACTTCCGAG 60.376 63.158 0.00 0.00 0.00 4.63
4451 4591 2.514824 GAATCTGGGTCTGCGGGC 60.515 66.667 0.00 0.00 0.00 6.13
4515 4655 1.475682 GAAGGCCTGCCATTTCTTCAG 59.524 52.381 5.69 0.00 38.92 3.02
4535 4675 1.699656 CGAAATGGCTGCTGTCCTCG 61.700 60.000 0.00 0.00 0.00 4.63
4690 4836 3.311596 CAGAATGATCATTTCAGCGAGCA 59.688 43.478 21.57 0.00 39.69 4.26
4745 4892 4.505970 CAGGGAGGGAGGGAGGGG 62.506 77.778 0.00 0.00 0.00 4.79
4748 4895 3.649652 AAGGCAGGGAGGGAGGGAG 62.650 68.421 0.00 0.00 0.00 4.30
4749 4896 3.626596 AAGGCAGGGAGGGAGGGA 61.627 66.667 0.00 0.00 0.00 4.20
4767 4914 3.524541 GGCCAAATCCAGCAACATTTAG 58.475 45.455 0.00 0.00 0.00 1.85
4777 4924 1.304713 AGCACAGGGCCAAATCCAG 60.305 57.895 6.18 0.00 46.50 3.86
4789 4936 1.884075 AACATGGCATGGCAGCACAG 61.884 55.000 29.49 15.56 35.83 3.66
4819 4966 5.802465 AGACCACATCATCATACATGATCC 58.198 41.667 0.00 0.00 45.23 3.36
4923 5084 3.794717 TGAGTACGTACAAGCCAACAAA 58.205 40.909 26.55 0.00 0.00 2.83
4934 5095 5.103000 AGCAGATCAATGTTGAGTACGTAC 58.897 41.667 18.10 18.10 41.08 3.67
4935 5096 5.324784 AGCAGATCAATGTTGAGTACGTA 57.675 39.130 0.00 0.00 41.08 3.57
4936 5097 4.177026 GAGCAGATCAATGTTGAGTACGT 58.823 43.478 0.00 0.00 41.08 3.57
4937 5098 3.553511 GGAGCAGATCAATGTTGAGTACG 59.446 47.826 0.00 0.00 41.08 3.67
5004 5165 2.111043 AACGACCACACAGCCAGG 59.889 61.111 0.00 0.00 0.00 4.45
5006 5167 0.178301 TAACAACGACCACACAGCCA 59.822 50.000 0.00 0.00 0.00 4.75
5009 5170 4.804608 TTGAATAACAACGACCACACAG 57.195 40.909 0.00 0.00 33.18 3.66
5010 5171 4.214545 GGATTGAATAACAACGACCACACA 59.785 41.667 0.00 0.00 41.52 3.72
5027 5188 3.010584 CCAGGAAGGAGAAAAGGGATTGA 59.989 47.826 0.00 0.00 41.22 2.57
5034 5195 2.373502 ACAGTCCCAGGAAGGAGAAAAG 59.626 50.000 0.00 0.00 41.22 2.27
5039 5200 1.209019 CATGACAGTCCCAGGAAGGAG 59.791 57.143 0.00 0.00 41.22 3.69
5040 5201 1.203300 TCATGACAGTCCCAGGAAGGA 60.203 52.381 0.00 0.00 41.22 3.36
5041 5202 1.209019 CTCATGACAGTCCCAGGAAGG 59.791 57.143 0.00 0.00 37.03 3.46
5054 5215 0.543749 AGGTAAGGCTGGCTCATGAC 59.456 55.000 3.48 0.79 0.00 3.06
5070 5242 1.528824 CAGGCCGAATGATGGAGGT 59.471 57.895 0.00 0.00 0.00 3.85
5071 5243 1.228063 CCAGGCCGAATGATGGAGG 60.228 63.158 0.00 0.00 34.60 4.30
5072 5244 0.107017 AACCAGGCCGAATGATGGAG 60.107 55.000 13.13 0.00 36.62 3.86
5073 5245 0.107214 GAACCAGGCCGAATGATGGA 60.107 55.000 13.13 0.00 36.62 3.41
5074 5246 0.394216 TGAACCAGGCCGAATGATGG 60.394 55.000 4.94 4.94 38.83 3.51
5075 5247 1.019673 CTGAACCAGGCCGAATGATG 58.980 55.000 0.00 0.00 0.00 3.07
5078 5686 3.190878 GCTGAACCAGGCCGAATG 58.809 61.111 0.00 0.00 31.21 2.67
5211 6088 0.743701 CTGGGATGCTCACTGCTGAC 60.744 60.000 0.00 0.00 43.37 3.51
5273 6150 8.822805 AGATCAGACCACCAACTTTATAAGTAA 58.177 33.333 0.00 0.00 41.91 2.24
5274 6151 8.375493 AGATCAGACCACCAACTTTATAAGTA 57.625 34.615 0.00 0.00 41.91 2.24
5276 6153 7.493971 CAGAGATCAGACCACCAACTTTATAAG 59.506 40.741 0.00 0.00 0.00 1.73
5277 6154 7.180229 TCAGAGATCAGACCACCAACTTTATAA 59.820 37.037 0.00 0.00 0.00 0.98
5278 6155 6.667848 TCAGAGATCAGACCACCAACTTTATA 59.332 38.462 0.00 0.00 0.00 0.98
5290 6167 1.422531 AGGCCATCAGAGATCAGACC 58.577 55.000 5.01 0.00 0.00 3.85
5294 6220 5.455755 CCAAATCTAAGGCCATCAGAGATCA 60.456 44.000 5.01 0.00 0.00 2.92
5295 6221 5.002516 CCAAATCTAAGGCCATCAGAGATC 58.997 45.833 5.01 0.00 0.00 2.75
5296 6222 4.202545 CCCAAATCTAAGGCCATCAGAGAT 60.203 45.833 5.01 2.12 0.00 2.75
5297 6223 3.137176 CCCAAATCTAAGGCCATCAGAGA 59.863 47.826 5.01 0.00 0.00 3.10
5298 6224 3.137176 TCCCAAATCTAAGGCCATCAGAG 59.863 47.826 5.01 0.00 0.00 3.35
5299 6225 3.122480 TCCCAAATCTAAGGCCATCAGA 58.878 45.455 5.01 4.22 0.00 3.27
5300 6226 3.582998 TCCCAAATCTAAGGCCATCAG 57.417 47.619 5.01 0.00 0.00 2.90
5302 6228 4.077822 CTGATCCCAAATCTAAGGCCATC 58.922 47.826 5.01 0.00 0.00 3.51
5303 6229 3.753193 GCTGATCCCAAATCTAAGGCCAT 60.753 47.826 5.01 0.00 0.00 4.40
5304 6230 2.423373 GCTGATCCCAAATCTAAGGCCA 60.423 50.000 5.01 0.00 0.00 5.36
5305 6231 2.234143 GCTGATCCCAAATCTAAGGCC 58.766 52.381 0.00 0.00 0.00 5.19
5306 6232 2.234143 GGCTGATCCCAAATCTAAGGC 58.766 52.381 0.00 0.00 0.00 4.35
5318 6244 0.846693 AGTAACATGGGGGCTGATCC 59.153 55.000 0.00 0.00 0.00 3.36
5319 6245 1.972872 CAGTAACATGGGGGCTGATC 58.027 55.000 0.00 0.00 0.00 2.92
5320 6246 0.106519 GCAGTAACATGGGGGCTGAT 60.107 55.000 11.29 0.00 0.00 2.90
5321 6247 1.207488 AGCAGTAACATGGGGGCTGA 61.207 55.000 11.29 0.00 0.00 4.26
5322 6248 1.033746 CAGCAGTAACATGGGGGCTG 61.034 60.000 11.00 11.00 42.14 4.85
5323 6249 1.207488 TCAGCAGTAACATGGGGGCT 61.207 55.000 0.00 0.00 0.00 5.19
5324 6250 1.032114 GTCAGCAGTAACATGGGGGC 61.032 60.000 0.00 0.00 0.00 5.80
5409 6335 1.043816 TGATCATTCGGCCTCCTCTC 58.956 55.000 0.00 0.00 0.00 3.20
5415 6341 1.369625 GTCGTTTGATCATTCGGCCT 58.630 50.000 16.18 0.00 0.00 5.19
5416 6342 0.026285 CGTCGTTTGATCATTCGGCC 59.974 55.000 15.39 0.00 0.00 6.13
5418 6344 1.989864 TCACGTCGTTTGATCATTCGG 59.010 47.619 16.18 7.22 0.00 4.30
5419 6345 2.222508 GGTCACGTCGTTTGATCATTCG 60.223 50.000 11.97 11.97 0.00 3.34
5440 6379 1.156736 GCATTTCATATCGGACCCGG 58.843 55.000 8.73 0.00 40.25 5.73
5443 6382 4.142600 GGCATAAGCATTTCATATCGGACC 60.143 45.833 0.00 0.00 44.61 4.46
5447 6386 6.815641 AGAGTAGGCATAAGCATTTCATATCG 59.184 38.462 0.00 0.00 44.61 2.92
5466 6405 5.312120 ACCGGATCGCATTATTAGAGTAG 57.688 43.478 9.46 0.00 0.00 2.57
5469 6408 5.466819 TGTAACCGGATCGCATTATTAGAG 58.533 41.667 9.46 0.00 0.00 2.43
5482 6421 0.179084 CGCCATCACTGTAACCGGAT 60.179 55.000 9.46 0.00 0.00 4.18
5486 6425 1.693083 GCGTCGCCATCACTGTAACC 61.693 60.000 5.75 0.00 0.00 2.85
5535 6475 2.026272 CGTTTAATTTGGCGTGCGAATG 59.974 45.455 0.00 0.00 0.00 2.67
5557 6500 6.015772 ACCAGAAAATATACGCACAGGTTTTT 60.016 34.615 0.00 0.00 0.00 1.94
5588 6535 3.064324 GCCAGCACCATCCACCAC 61.064 66.667 0.00 0.00 0.00 4.16
5595 6542 1.401318 TTTGCAACTGCCAGCACCAT 61.401 50.000 0.00 0.00 41.05 3.55
5596 6543 1.611474 TTTTGCAACTGCCAGCACCA 61.611 50.000 0.00 0.00 41.05 4.17
5597 6544 0.877213 CTTTTGCAACTGCCAGCACC 60.877 55.000 0.00 0.00 41.05 5.01
5598 6545 0.877213 CCTTTTGCAACTGCCAGCAC 60.877 55.000 0.00 0.00 41.05 4.40
5599 6546 1.442567 CCTTTTGCAACTGCCAGCA 59.557 52.632 0.00 0.00 41.18 4.41
5600 6547 1.957695 GCCTTTTGCAACTGCCAGC 60.958 57.895 0.00 0.00 41.18 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.